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Metabolomics Intro

The CCPN Project for metabolite NMR data

With Francesca Chignola, Silvia Mari & Giovanna Musco, San Raffaele Scientific Institute, Milano, Italia

13C HSQC metabolite spectra

Many of the spectrum visualisation routines, chemical compound descriptions and assignment tools that have already been developed in CCPN for macromolecules are directly applicable to NMR studies of small metabolite compounds. In order to improve the resources within CCPN for the study of metabolite spectra Francesca Chignola and Silvia Mari have used CcpNmr Analysis to create a CCPN project containing the resonance assigned 13C HSQC spectra from more than 35 common metabolites. This metabolomics CCPN project is available to download via the following links (both 383MB, including spectra): CCPN_Metabolomic_v1.3.tar.gz (Linux/Mac) CCPN_Metabolomic_v1.3.zip (Windows) . To help users get started with metabolomic analyses using this CCPN project a tutorial guide is also available as a PDF document here: CcpnMetabolomicsTutorial.pdf

In the future we will be extending CCPN functionality specifically for NMR based metabolite studies. The objective in the initial instance is to provide an efficient tool for the identification and assignment of metabolites within mixtures by comparing 2D H-C and H-H spectra with reference assignments. The metabolite screening procedure will be underpinned by the NmrScreen package of the CCPN data model; the same multi-purpose package that will also support industrial small ligand screening.

 

Quick links:

CCPN Metabolomics Project Data (.tar.gz) - An tar gzipped archive containing the CCPN Metabolomics project data; both spectra and CCPN project.

CCPN Metabolomics Project Data (.zip) - A Windows .zip file containing the CCPN Metabolomics project, including spectra

Metabolomics Tutorial Script - A PDF file containing a tutorial to illustrate the use of the CCPN Metabolomics project

Synthetic TOCSY Macro - A Python macro script for CcpNmr Analysis to generate synthetic HH TOCSY peak lists given 13CHSQC assignments

Assign Closest Metabolite Peak Script - Example Python script to automatically assign a query peak list, representing a sample with a mixture of metabolites, using reference metabolite assignments from the CCPN Metabolomics Project.

Python API Programming Guide - A course to illustrate how to write scripts that use the CCPN Python API.